There are a number of ways in which we can make this argument. Let us look at two of the more important of these.
First, we can argue that it is not immoral for Native Americans to use hallucinogens because the drugs do not hurt anyone other than, possibly, the person who takes them. The idea that doing harmful things to one’s own body is immoral is something that comes from specific religious traditions. It is not something (like the idea that murder is wrong) that is obvious to most people. We can argue that we should not hold Native American populations to a set of moral beliefs that are not their own.
Second, we can argue that Native Americans do not use peyote and other hallucinogens for immoral purposes. We can argue that using drugs for recreation is immoral because it has no real value. There is no reason for taking these drugs other than to have “fun.” By contrast, Native Americans use hallucinogens for a higher purpose. Because they are using the drugs as part of their religion, they are not acting immorally when they do so.